Contacts of the helix formed by residues 184 - 200 (chain B) in PDB entry 6F0X
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 184 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LEU* 4.9 2.6 - - - +
141B TYR* 4.1 1.3 - - - -
183B THR* 1.3 49.2 - - - +
185B LYS* 1.3 52.3 - - - -
187B SER* 2.8 7.5 + - - -
188B LEU* 2.4 36.7 + - - -
901B AGS 1.3 88.5 + - - -
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Residues in contact with LYS 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 3.8 16.8 - - + +
178B HIS* 3.5 29.2 - - - +
179B GLY* 3.5 29.2 - - - +
183B THR* 2.9 22.9 + - + +
184B GLY* 1.3 65.8 - - - +
186B THR* 1.3 56.1 + - - +
188B LEU* 3.4 11.3 - - + +
189B CYS* 2.9 35.3 + - - -
298B THR* 3.7 19.5 - - + -
299B SER 4.1 3.4 - - - +
300B ASN* 2.3 41.8 + - - +
319B ILE* 5.1 7.2 - - + -
901B AGS 2.3 26.2 + - - +
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Residues in contact with THR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLY 2.8 0.6 + - - -
185B LYS* 1.3 80.2 - - - +
187B SER* 1.3 64.9 + - - +
189B CYS* 3.1 5.4 + - - +
190B LYS* 3.0 33.2 + - - +
211B GLU* 4.5 10.1 - - - +
250B LEU* 4.3 21.7 - - + +
252B ASP* 4.0 19.5 + - - +
298B THR* 4.0 11.6 + - - +
901B AGS 2.9 30.3 + - - -
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Residues in contact with SER 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PHE* 5.9 1.3 - - - -
135B LEU* 4.0 14.1 - - - +
139B LEU* 3.7 12.7 - - - +
184B GLY* 2.8 9.4 + - - -
186B THR* 1.3 77.1 - - - +
188B LEU* 1.3 59.8 + - - +
190B LYS* 3.4 21.1 + - - +
191B ALA* 2.8 30.5 + - - +
901B AGS 3.6 14.8 + - - -
288C LYS* 5.3 6.2 + - - -
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Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B TRP* 4.4 17.9 - - + -
139B LEU* 3.6 23.7 - - + +
141B TYR* 3.5 42.4 - - + +
145B VAL* 5.9 3.6 - - + -
146B LYS* 5.4 3.1 - - + -
149B LEU* 5.5 6.7 - - + -
177B LEU* 3.8 25.4 - - + -
184B GLY 2.4 32.8 + - - +
185B LYS* 3.4 11.4 - - + +
187B SER* 1.3 69.1 - - - +
189B CYS* 1.3 57.8 + - - +
191B ALA* 3.2 1.7 + - - +
192B LEU* 2.9 27.4 + - + +
319B ILE* 5.1 8.3 - - + -
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Residues in contact with CYS 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 5.9 1.3 - - - -
177B LEU* 4.4 19.1 - - - -
185B LYS 2.9 18.3 + - - -
186B THR 3.1 7.6 + - - +
188B LEU* 1.3 75.0 - - - +
190B LYS* 1.3 64.5 + - - +
192B LEU* 3.1 7.0 + - - +
193B ALA* 2.9 22.5 + - - +
250B LEU* 4.1 11.7 - - + -
296B LEU* 3.5 47.9 - - + +
297B THR 4.8 0.2 - - - -
298B THR* 4.0 17.3 - - - -
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Residues in contact with LYS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B TRP* 3.7 20.5 - - - -
132B PHE* 3.4 46.5 - - + -
135B LEU* 4.9 1.3 - - + -
186B THR* 3.0 23.7 + - - +
187B SER* 3.2 25.1 + - - +
189B CYS* 1.3 77.2 - - - +
191B ALA* 1.3 57.2 + - - +
193B ALA* 3.0 10.3 + - - +
194B GLN* 2.9 26.6 + - - +
209B LEU* 4.5 10.0 - - + +
211B GLU* 3.4 27.9 + - - -
250B LEU* 4.3 14.6 - - + -
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Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PHE 5.8 0.2 - - - -
135B LEU* 3.8 27.3 - - + +
136B TRP* 3.7 30.1 - - + +
139B LEU* 4.0 7.2 - - + -
187B SER 2.8 16.9 + - - +
188B LEU 3.6 4.0 - - - +
190B LYS* 1.3 72.9 - - - +
192B LEU* 1.3 66.9 + - - +
194B GLN* 3.2 7.2 + - - +
195B LYS* 2.8 26.0 + - - +
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Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B TRP* 3.9 18.0 - - + -
149B LEU* 3.6 52.7 - - + +
150B LEU* 4.2 15.5 - - + +
153B VAL* 5.5 2.7 - - + -
188B LEU 2.9 12.5 + - - +
189B CYS* 3.2 9.4 - - - +
191B ALA* 1.3 76.3 - - - +
193B ALA* 1.3 64.4 + - - +
195B LYS* 3.2 2.3 + - + +
196B LEU* 2.9 49.2 + - + +
248B PHE* 4.7 2.5 - - + -
294B VAL* 5.6 1.6 - - + -
296B LEU* 3.5 26.5 - - + -
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Residues in contact with ALA 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 4.7 6.1 - - + +
189B CYS 2.9 12.4 + - - +
190B LYS* 3.0 12.8 + - - +
192B LEU* 1.3 78.2 - - - +
194B GLN* 1.3 52.8 + - - +
196B LEU 3.3 0.2 + - - -
197B THR* 2.4 38.2 + - - -
209B LEU* 4.8 10.3 - - + -
248B PHE* 3.4 47.0 - - + -
296B LEU* 5.6 0.2 - - + -
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Residues in contact with GLN 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PHE* 4.4 7.7 - - - -
102B LEU* 4.9 0.4 - - - +
127B LEU 2.8 13.3 - - - +
128B PRO* 3.2 15.0 - - - +
129B ALA* 2.4 48.2 + - - +
132B PHE* 4.2 24.0 - - + +
133B HIS* 5.4 1.8 - - - +
136B TRP* 6.4 0.4 - - + -
190B LYS 2.9 12.3 + - - +
191B ALA* 3.2 9.2 + - - +
193B ALA* 1.3 76.4 - - - +
195B LYS* 1.3 64.1 + - - +
197B THR* 3.0 7.8 - - - +
198B ILE* 3.0 46.1 + - + +
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Residues in contact with LYS 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 1.9 45.3 + - + +
74B SER* 5.1 0.6 + - - -
76B ILE* 5.1 10.4 - - - +
136B TRP* 3.4 47.8 - - + +
137B ASP* 5.2 2.4 + - - -
150B LEU* 3.9 24.5 - - + -
191B ALA 2.8 17.6 + - - +
192B LEU* 3.6 5.6 - - - +
194B GLN* 1.3 78.4 - - - +
196B LEU* 1.3 63.0 + - - +
197B THR 3.2 0.2 + - - -
198B ILE* 3.3 1.8 + - + +
199B ARG* 2.9 41.1 + - - +
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Residues in contact with LEU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B LEU* 3.6 29.4 - - + +
153B VAL* 3.8 37.5 - - + -
154B MET* 4.8 3.6 - - + +
192B LEU* 2.9 28.7 + - + +
193B ALA 3.7 3.4 - - - +
195B LYS* 1.3 75.6 - - - +
197B THR* 1.3 63.9 + - - +
199B ARG* 3.0 8.2 + - + +
200B LEU* 2.9 45.2 + - + +
246B LEU* 4.5 4.7 - - + +
248B PHE* 3.4 35.0 - - + -
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Residues in contact with THR 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PHE* 5.7 1.3 - - + -
127B LEU* 3.0 45.0 + - + +
128B PRO* 3.8 29.2 - - + -
193B ALA 2.4 24.0 + - - -
194B GLN* 3.0 16.0 - - - +
196B LEU* 1.3 78.0 - - - +
198B ILE* 1.3 67.1 + - + +
199B ARG 3.2 0.2 + - - -
200B LEU* 3.3 8.0 + - - +
201B SER* 4.0 7.6 + - - -
204B TYR 5.5 0.2 - - - +
206B TYR* 6.2 1.6 - - - -
246B LEU* 5.0 2.9 - - - +
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Residues in contact with ILE 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLU* 3.6 42.8 - - + +
98B HIS* 3.2 31.7 + - + +
99B ILE 5.0 1.8 - - - +
100B PHE* 3.4 64.2 - - + -
133B HIS* 5.7 1.1 - - - +
194B GLN* 3.0 28.4 + - + +
195B LYS* 4.0 3.1 - - + +
197B THR* 1.3 81.1 - - + +
199B ARG* 1.3 63.1 + - - +
200B LEU 3.4 0.3 + - - -
201B SER* 4.1 7.2 + - - -
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Residues in contact with ARG 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B HIS* 2.9 64.4 + - - +
98B HIS* 3.1 41.5 + - - -
150B LEU* 3.8 30.8 - - - +
154B MET* 3.5 36.2 - - - +
195B LYS* 2.9 34.8 + - - +
196B LEU* 3.0 11.4 + - + +
198B ILE* 1.3 78.4 - - - +
200B LEU* 1.3 67.4 + - + +
201B SER 3.5 1.4 + - - -
202B SER* 4.7 2.3 + - - -
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Residues in contact with LEU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 4.4 15.7 - - + +
154B MET* 3.9 21.1 - - + -
157B LEU* 5.6 3.6 - - + -
196B LEU* 2.9 39.3 + - + +
197B THR 3.3 5.1 + - - +
199B ARG* 1.3 98.3 - - + +
201B SER* 1.3 51.8 + - - +
202B SER* 3.3 9.2 - - - +
203B ARG* 3.9 15.3 - - + +
204B TYR* 2.7 58.8 + - + +
246B LEU* 4.7 11.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il